Mercurial > repos > elixir-it > covacs_apply_recalibrator
changeset 2:f47e8d9b7f2e draft default tip
Uploaded
| author | elixir-it |
|---|---|
| date | Wed, 02 Oct 2019 04:29:44 -0400 |
| parents | 48dc4c9bc497 |
| children | |
| files | covacs_ApplyRecalibrator.xml mv_untar_gatk.sh |
| diffstat | 2 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/covacs_ApplyRecalibrator.xml Thu Nov 15 15:54:51 2018 -0500 +++ b/covacs_ApplyRecalibrator.xml Wed Oct 02 04:29:44 2019 -0400 @@ -1,5 +1,5 @@ <tool id="covacs_ApplyRecalibrator" name="covacs_ApplyRecalibrator" version="3.8"> - <description>gatk ApplyRecalibrator wrapper </description> + <description>gatk ApplyRecalibrator wrapper for covacs</description> <macros> <import>bed_macros.xml</import> </macros> @@ -9,7 +9,7 @@ <command> <![CDATA[ ### call the .sh to untar the package - sh $__tool_directory__/mv_untar_gatk.sh && + bash $__tool_directory__/mv_untar_gatk.sh &> $log &&
--- a/mv_untar_gatk.sh Thu Nov 15 15:54:51 2018 -0500 +++ b/mv_untar_gatk.sh Wed Oct 02 04:29:44 2019 -0400 @@ -1,9 +1,10 @@ #!/bin/bash #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm #and untar the archive -if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then +if [ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ] ; then + echo start untar ; tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar - + echo all done else echo GATK is present fi